Glycobiology 1st Edition by Minoru Fukuda 0123809991 9780123810007

Volume in series

Auxiliary and Autonomous Proteoglycan Signaling Networks

1. Overview of Proteoglycan Structure, Nomenclature, and Function

2. Growth Factor Signaling

3. Integrin Interactions

4. Autonomous Signaling

5. Proteoglycan Downregulation: Endocytosis and Ectodomain Shedding

6. Cell Adhesion

7. Migration

8. Experimental Procedures

Acknowledgments

Dual Roles of Drosophila Glypican Dally-Like in Wingless/Wnt Signaling and Distribution

1. Introduction

2. Generation of Dally and Dlp Null Alleles

3. Examination of Dally and Dlp in Wg Signaling and Gradient Formation in the Wing Disc

4. Dlp Core Protein Determines Its Biphasic Activity in Wg Morphogen Signaling

5. Dlp Core Protein Can Interact with Wg Independent of Its GAG Chains

6. The Ratio of Dlp/Fz2 Determines the Biphasic Activity of Dlp or Dlp Core Protein in Wg Signaling

7. Conclusion

Acknowledgments

Use of a Phage Display Antibody to Measure the Enzymatic Activity of the Sulfs

1. Overview

2. ELISA for Sulf Activity Against the RB4CD12 Epitope in Immobilized Heparin/HS

3. Flow Cytometry-Based Sulf Assay Against the Cell Surface RB4CD12 Epitope

4. Ex Vivo Sulf Assay Against the RB4CD12 Epitope in Cryostat-Cut Sections

Acknowledgments

Glycomics Profiling of Heparan Sulfate Structure and Activity

1. Overview

2. Experimental

3. Conclusions and Future Perspectives

Acknowledgments

Microbe-Associated Molecular Patterns in Innate Immunity

Abbreviation list

1. Overview

2. LPS and LOS Extraction Procedures

3. Purification of the Crude Extracts

4. SDS-PAGE

5. Carbohydrate Analysis: Monosaccharide Determination, Absolute Configuration, and Definition of Branching Points

6. Fatty Acids Compositional Analysis (GC-MS)

Structural and Functional Analysis of Glycosphingolipids of Schistosoma mansoni

1. Overview

2. Isolation and Purification of S. mansoni Glycosphingolipids

3. Structural Characterization of S. mansoni Glycosphingolipids

4. Immunochemical Characterization of Glycan Antigens

5. Interaction of S. mansoni Glycosphingolipids with Dendritic Cell Receptors

6. Conclusions

Biotoxicity Assays for Fruiting Body Lectins and Other Cytoplasmic Proteins

1. Overview

2. Expression of Fruiting Body Lectins in E. coli

3. Toxicity Test Toward the Insect A. aegypti

4. Toxicity Test Toward the Nematode C. elegans

5. Toxicity Test Toward the Amoeba A. castellanii

6. Statistics

Acknowledgments

Carbohydrate Signaling by C-Type Lectin DC-SIGN Affects NF-κB Activity

1. Overview

2. Dendritic Cell Stimulation with LPS and ManLAM

3. RNA Interference in Dendritic Cells

4. NF-κB Activation in DCs

5. Phosphorylation and Acetylation of NF-κB by DC-SIGN Signaling

6. Activity of Acetyltransferases in DC

7. Transcription Regulation by Acetylation of p65

8. Concluding Remarks

Acknowledgments

Engineered Carbohydrate-Recognition Domains for Glycoproteomic Analysis of Cell Surface Glycosylation and Ligands for Glycan-Binding Receptors

1. Overview

2. Engineering Glycan-Binding Specificity

3. CRDs as Probes for Detection of Glycans on Blots

4. CRDs as Affinity Tools for Probing of Cell Surface Glycosylation

Acknowledgments

Mannose 6-Phosphate Receptor Homology Domain-Containing Lectins in Mammalian Endoplasmic Reticulum-Associated Degradation

1. Overview

2. Quality Control of Newly Synthesized Glycoproteins

3. Primary Structures of Yos9p, OS-9, and XTP3-B

4. OS-9 and XTP3-B form a Complex with Membrane-Embedded Ubiquitin Ligase

5. Sugar Recognition Specificity of OS-9 and XTP3-B

6. The Effect of OS-9 and XTP3-B on ERAD in Mammals

7. Concluding Remarks

Acknowledgments

Multiple Functional Targets of the Immunoregulatory Activity of Galectin-1

1. General Introduction

2. Regulation of Immune Cell Trafficking, Recruitment, and Chemotaxis

3. Galectin–Glycan Lattices in the Control of DC Physiology

4. Galectin–Glycan Lattices in the Control of T Helper Cell Fate

5. Final Remarks and Future Directions

Acknowledgments

Manipulating Cell Surface Glycoproteins by Targeting N-Glycan–Galectin Interactions

1. Overview

2. Galectins and Their N-Glycan Ligands

3. Regulation of Glycoprotein Concentration at the Cell Surface by the Galectin–Glycoprotein Lattice

4. T Cells and the Galectin–Glycoprotein Lattice

5. Genetic and Metabolic Regulation of the Galectin–Glycoprotein Lattice

6. Overview of Methods to Measure and Modulate the Galectin–Glycoprotein Lattice

Galectin-1 and HIV-1 Infection

1. Overview

2. Experimental

The Glycomics of Glycan Glucuronylation in Drosophila melanogaster

1. Introduction

2. Experimental Procedures and Results

3. Discussion

Acknowledgments

Glycosyltransferases and Transporters that Contribute to Proteoglycan Synthesis in Drosophila

1. Overview of Glycosaminoglycan Biosynthesis in Drosophila

2. Identification of Drosophila Glycosyltransferases and Sugar-Nucleotide Transporters that Contribute to Proteoglycan Synthesis

3. Establishment and Functional Analysis of RNAi Flies for the Glycosyltransferases and Sugar-Nucleotide Transporters that Contribute to Proteoglycan Synthesis

O-GlcNAc Modification of the Extracellular Domain of Notch Receptors

1. Overview

2. Preparation of Recombinant EGF Domains by Yeast Expression System

3. In Vitro O-GlcNAc Transferase Assay

4. Mass Spectrometry

5. Detection of O-β-GlcNAc Modification Using Antibodies

6. Galactosyltransferase Labeling

7. Hexosaminidase Treatment

8. Conclusions and Future Directions

Acknowledgments

Regulation of Notch Signaling Via O-Glucosylation

1. Overview

2. Genetic Identification and Characterization of rumi

3. Drosophila Strains

4. Drosophila Culture and Husbandry

5. A Genetic Screen to Identify New Notch Regulators

6. Mapping and Sequencing

7. Rescue Experiments

8. Generation of a Protein-Null Allele of rumi Via P-Element Excision

9. Experimental Evidence that Rumi is a Protein O-Glucosyltransferase

10. Enzyme Assay for Protein O-Glucosyltransferase Activity

11. Analysis of the Product Obtained from the Protein O-Glucosyltransferase Assay

12. Detection of O-Linked Glucose on Notch EGF Repeats by Mass Spectrometry

Acknowledgments

O-Fucosylation of Thrombospondin Type 1 Repeats

1. Overview

2. Glycosylation Site Mapping by Mass Spectrometry

Acknowledgments

Use of Glycan Microarrays to Explore Specificity of Glycan-Binding Proteins

1. Overview

2. The Printed Glycan Microarray from the Consortium for Functional Glycomics (CFG)

3. Analysis of GBPs on the CFG Glycan Microarray

4. Defining a Glycan Motif Using Concentration-Dependent Binding of GBPs to the Printed Glycan Microarray

5. The Concentration-Dependent Binding of Sambucus nigra Agglutinin to the Printed Glycan Microarray and a Method for Ranking the Relative Binding Strengths to Glycan Ligands

6. Using Microarrays to Identify a Glycan-Binding Motif for SNA

7. Specificities of Human Galectin-8 and its Carbohydrate Recognition Domains (CRDs)

8. Challenges in Identifying Physiological Ligands for GBPs

9. Conclusion and Future Directions

Acknowledgments

Functional Roles of the Bisecting GlcNAc in Integrin-Mediated Cell Adhesion

1. Overview

2. Manipulation of GnT-III and GnT-V Genes in Cancer Cells

3. Assays for Cell Spreading and Migration

4. Construction of Various Integrin α5β1 Mutants by the Mutagenesis of Potential N-Glycosylation Sites

5. N-Glycans Differentially Regulate Integrin-Mediated Cell Adhesion and Migration

6. Identification of Important N-Glycosylation Sites for Functional Expression of α5β1 Integrin

7. Site-4 Is a Crucial N-Glycosylation Site on the α5 Subunit for GnT-III Regulation

8. Future Perspectives

Acknowledgments

Lectin-Based Glycoproteomic Techniques for the Enrichment and Identification of Potential Biomarkers

1. Introduction

2. Lectin Blotting and Separation of Total Glycoproteins in a Sample Using a Lectin(s) Immobilized on Paramagnetic Beads

3. Separation of Glycoproteins Using a Lectin Immobilized on Paramagnetic Beads Prior to Mass Spectrometry-Based Shotgun Proteomics

4. Glycomics Strategy for Identifying Potential Glycoprotein Cancer Markers

5. MS/MS Data Analysis and Confirmation of Glycoprotein Glycosylation Differences When Results from Two Tissue Sources are Compared

6. Conclusions

Acknowledgments

High-Throughput RNAi Screening for N-Glycosylation Dependent Loci in Caenorhabditis elegans

1. Overview

2. N-glycosylation in C. elegans

3. RNAi in C. elegans

4. C. elegans Strains, Culturing and RNAi Methods

5. Genome-wide RNAi Screen

6. Discussion

The Acidic Environment of the Golgi Is Critical for Glycosylation and Transport

1. Introduction

2. Reporter Proteins for Transport Monitoring

3. Establishment of Parent Cells for Screening Transport Mutant Cells

4. Transport Assay of Reporter Proteins

5. Application of Transport Assay

6. Mutagenesis

7. Selection of Mutant Cells

8. Measurement of Golgi pH

9. Analysis of Glycosylation Using Lectin Staining

10. Concluding Remarks

Acknowledgment

Enzymatic Synthesis of Lacto-N-Difucohexaose I Which Binds to Helicobacter pylori

1. Overview

2. Synthesis of Lacto-N-triose II Using β-1,3-N-Acetylglucosaminyltransferase

3. Synthesis of Lacto-N-tetraose by Transglycosylation Using β-1,3-Galactosidase

4. Preparation of Recombinants FUT1 and FUT3

5. Synthesis of Lacto-N-fucopentaose I and Lacto-N-difucohexaose I with the Aid of Fucosyltransferases

Acknowledgments

The Drosophila 7-Pass Transmembrane Glycoprotein BOSS and Metabolic Regulation

1. Introduction

2. BOSS: Drosophila Orphan Membrane Receptor

3. BOSS Responds to Extracellular Glucose

4. Sugar and Lipid Metabolism Is Impaired in boss Null Mutants

5. boss Mutant Flies Are Sensitive to Starvation

6. Biochemical Techniques for Detecting TAG